Long Noncoding RNAs as Therapeutic and Diagnostic Markers for Childhood Cancer Medulloblastoma

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Unmet Need

Medulloblastoma (MB) is the most common pediatric brain tumor and requires aggressive therapy in high-risk cases. MB is frequently resistant to treatment and is associated with high morbidity and mortality in affected individuals. There are four distinct molecular subgroups of MB (WNT, SHH, Group 3, and Group 4), which are characterized by specific mutations, copy number alterations, transcriptomic profiles, and clinical outcomes. Patients diagnosed with the WNT subgroup have the highest 5 year survival rates (~95% survival) while group 3 patients have the worst (45-60% survival). The WNT and SSH subgroups have clearly defined molecular phenotypes; however, there are currently no definitive characterizations of Group 3 and Group 4 subgroups. Due to the severity of the disease and the poor prognoses associated with patients affected with Group 3 MBs, there is a need for sensitive diagnostic tests capable of identifying these high-risk individuals so proper treatment can be carried out immediately.

Technology Overview

Johns Hopkins researchers have identified specific long noncoding RNAs (lncRNAs) that can differentiate MB subgroups with greater accuracy than current methods by analyzing 723 microarray and 123 RNA-seq MB datasets with machine-learning statistical algorithms. The newly identified lncRNAs were shown to be upregulated in Group 3 MBs when compared to other MB subgroups. The researchers confirmed these lncRNAs were specific to Group 3 over other subgroups or healthy brain tissue using RNA-FISH probes. Moreover, the researchers demonstrated that MB cells that have the Group 3-specific lncRNA knocked out have significantly reduced cell growth and increased apoptosis. Thus, these newly identified lncRNAs can be used as potential diagnostic markers and therapeutic targets for children with Group 3 MB.

Stage of Development

The inventors have created CRISPR knockouts in MB mammalian cell lines of specific lncRNAs that are unique to Group 3 MB. LncRNA depleted cell lines show a dramatic reduction in in vivo tumor growth in mouse brain (cerebellum) confirm its potential as a therapeutic target. The inventors have also developed a panel of Group II and IV lncRNAs to test medulloblastoma specifically via RNA-FISH in solid tumor samples and by qPCR and digital PCR (ddPCR) in cerebral spinal fluid (CSF). 


  1. Perera, et. al., bioRxiv. In silico analysis of long non-coding RNAs in medulloblastoma and its subgroups. 783092
  2. JHU Press release December 2020
Patent Information:
Title App Type Country Serial No. Patent No. File Date Issued Date Expire Date Patent Status
USE OF LONG NON-CODING RNAS IN MEDULLOBLASTOMA PCT: Patent Cooperation Treaty United States 17/642,752   3/14/2022     Pending
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